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EZH2 Mediates Epigenetic Silencing of Neuroblastoma Suppressor Genes CASZ1, CLU, RUNX3 and NGFR

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EZH2 Mediates Epigenetic Silencing of Neuroblastoma Suppressor Genes CASZ1, CLU, RUNX3 and NGFR Author Manuscript Published OnlineFirst on November 8, 2011; DOI: 10.1158/0008-5472.CAN-11-0961 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. EZH2 mediates epigenetic silencing of neuroblastoma suppressor genes CASZ1, CLU, RUNX3 and NGFR Chunxi Wang1, Zhihui Liu1, Chan-Wook Woo1, Zhijie Li 1, Lifeng Wang5, Jun S. Wei2, Victor E. Marquez3, Susan E. Bates4, Qihuang Jin5, Javed Khan2, Kai Ge5 and Carol J. Thiele1* 1Cell & Molecular Biology Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD 2Oncogenomics Section, Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD 3Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 4 Molecular Therapeutics Section, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD 5Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney, National Institutes of Health, Bethesda, MD *: Address correspondence to: Carol J. Thiele (E-mail: [email protected], Tel: 301-496-1543) Running title: Tumor suppressor genes are regulated by EZH2 in NB Keywords: CASZ1, neuroblastoma, EZH2, NGFR, CLU, RUNX3 Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2011 American Association for Cancer Research. Author Manuscript Published OnlineFirst on November 8, 2011; DOI: 10.1158/0008-5472.CAN-11-0961 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Abstract Neuroblastoma (NB) is the most common extracranial pediatric solid tumor with an undifferentiated status and generally poor prognosis, but the basis for these characteristics remains unknown. In this study, we show that upregulation of the Polycomb complex histone methytransferase EZH2, which limits differentiation in many tissues, is critical to maintain the undifferentiated state and poor prognostic status of NB by epigenetic repression of multiple tumor suppressor genes. We identified this role for EZH2 by examining the regulation of CASZ1, a recently identified NB tumor suppressor gene whose ectopic restoration inhibits NB cell growth and induces differentiation. Reducing EZH2 expression by RNAi-mediated knockdown or pharmacological inhibiton with 3- deazaneplanocin A (DZNep) increased CASZ1 expression, inhibited NB cell growth and induced neurite extension. Similarly, EZH2-/- mouse embryonic fibroblasts (MEFs) displayed 3-fold higher levels of CASZ1 mRNA compared to EZH2+/+ MEFs. In cells with increased expression of CASZ1, treatment with HDAC inhibitors decreased expression of EZH2 and the Polycomb complex component SUZ12. Under steady-state conditions H3K27me3 and PRC2 components bound to the CASZ1 gene were enriched, but this enrichment was decreased after HDAC inhibitor treatment. We determined that the tumor suppressors CLU, NGFR and RUNX3 were also directly repressed by EZH2 like CASZ1 in NB cells. Together, our findings establish that aberrant upregulation of EZH2 in NB cells silences several tumor suppressors, which contribute to the genesis and maintenance of the undifferentiated phenotype of NB tumors. Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2011 American Association for Cancer Research. Author Manuscript Published OnlineFirst on November 8, 2011; DOI: 10.1158/0008-5472.CAN-11-0961 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Precis Dysregulation of a single targetable histone methyltransferase is found to be a core contributor to neuroblastoma phenotypes, highlighting a novel general approach to treat this common and deadly pediatric tumor. Introduction Neuroblastoma (NB) is the most common extracranial solid tumor in childhood, and accounts for 15% of all pediatric oncology deaths (1-3). Biological and genetic features have been used to stratify patients for risk and more intensive treatment. Biological features such as tumor histopathology or the Shimada classification system have revealed that undifferentiated or stroma-poor tumors have a worse prognosis than ganglioneuromas, which are mature, stroma rich tumors containing more differentiated ganglion cells. Patients with ganglioneuroblastomas, tumors that contain a spectrum of elements seen in both undifferentiated as well as well-differentiated tumors, have variable prognoses. Recent microarray analyses indicate the transcriptome of tumors from patients with poor prognoses is enriched in cell cycle related genes, while that of tumors from patients who have favorable prognoses tumors is enriched in differentiation-associated genes (4). The mechanisms by which the genetic alterations associated with neuroblastoma contribute to the undifferentiated state of NB are still unknown. A number of genetic alterations are associated with NB and are thought to affect the differentiation potential of the pluripotent sympathetic neuroblasts from which neuroblastomas are thought to arise. Patients whose neuroblastoma tumors contain genomic MYCN amplification and allelic deletion of the short arm of chromosome 1 Tumor suppressor genes are regulated by EZH2 in NB 3 Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2011 American Association for Cancer Research. Author Manuscript Published OnlineFirst on November 8, 2011; DOI: 10.1158/0008-5472.CAN-11-0961 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. (Chr1p deletion) have the highest risk and worst prognoses (reviewed in (2)). Chr1p deletion is highly correlated with MYCN amplification (5). Loss of heterozygosity of 1p36 (1p36LOH) is found in 20%-40% cases and is independently associated with progression-free survival (6). The consistent loss of 1p36 brought attention to this region as the site of a putative NB tumor suppressor gene (2, 3). Genes in the 1p36 region such as CHD5 (7, 8), miR-34a (9), TP73 (10) and most recently CASZ1, a neuronal differentiation gene, have been shown to possess tumor suppressor activity (11). CASZ1 is the human homologue of the drosophila zinc finger transcriptional factor Castor. Drosophila castor (cas) is specifically expressed in a subset of central nervous system (CNS) neuroblasts, and regulates late stage neurogenesis and neural fate determination (12). Liu et.al report that the level of human CASZ1 expression increases upon the induction of differentiation in NB cells and mesenchymal cells (13). The restoration of CASZ1 expression in NB cells inhibits cell proliferation in vitro and decreases tumor growth in vivo (11). In an evaluation of primary NB tumors, the expression of CASZ1 is significantly decreased in aggressive NB compared with the favorable tumors (14, 15). The finding that no tumor-associated nucleotide mutation is found in the coding sequence of CASZ1 (15, 16) suggests that mechanisms such as epigenetic silencing may be involved in the decreased expression of CASZ1 in tumors of patients with unfavorable prognoses. Major mechanisms of epigenetic silencing of gene expression include regulation of DNA methylation and the posttranslational modifications of histones. DNA methylation on the 1p36 region has been shown to mediate silencing of CHD5 in NB tumors cells (8). However, no consistent CpG methylation site in the 5’ proximal region Tumor suppressor genes are regulated by EZH2 in NB 4 Downloaded from cancerres.aacrjournals.org on September 26, 2021. © 2011 American Association for Cancer Research. Author Manuscript Published OnlineFirst on November 8, 2011; DOI: 10.1158/0008-5472.CAN-11-0961 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. or first intron of CASZ1 has been identified in either NB cell lines or primary tumors that differs from normal tissues (11, 15, 16). Thus it is unlikely that DNA methylation accounts for low CASZ1 expression in NB cells. The findings that the histone deacetylase inhibitors, depsipeptide (11) and trichostatin A (15) induce CASZ1 expression in NB cells, suggest that suppressive histone modifications inhibit CASZ1 gene expression. Histone acetylation tightly associates with gene activation and the trimethylation of histone 3 on lysine 27 (H3K27me3) is a well-known histone mark associated with gene silencing. H3K27me3 is mediated by the methyltransferase EZH2, which is the enzymatically active component of the Polycomb Repressor Complex 2 (PRC2) (17). PRC2 contains three core subunits, enhancer of zeste 2 (EZH2), embryonic ectoderm development (EED) and suppressor of zeste 12 homolog (SUZ12) (reviewed in (18-20)). EZH2 is essential for stem cell identity and pluripotency (reviewed in (18-20)). PRC2 regulates a large set of developmental genes in embryonic stem cells, such as the HOX gene clusters, SOX, PAX and WNT gene families. In retinoic acid (RA) induced neural stem cell differentiation, EZH2 expression is decreased in differentiated neural cells, consistent with decreased binding of EZH2 to RA-inducible target genes (reviewed in (18). While PRC2 is released from genes (HOXA 1-5, ZIC1, CKM) expressed during the differentiation, it is also recruited to the certain genes (HOXA9-13, Neroug2, Olig2) that may be suppressed in specific cell lineages (reviewed in (19)). This dynamic recruitment and displacement of PRC2 together with the tissue specific transcriptional
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